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Yorodumi- PDB-6u57: KDO8PS Structure Determined at the EuXFEL using Segmented Flow In... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u57 | ||||||||||||
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Title | KDO8PS Structure Determined at the EuXFEL using Segmented Flow Injection | ||||||||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||||||||
Keywords | TRANSFERASE / Catalytic Activity / Transferase Activity | ||||||||||||
Function / homology | Function and homology information 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / protein-containing complex / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Botha, S. / Ros, A. | ||||||||||||
Funding support | United States, Germany, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Segmented flow generator for serial crystallography at the European X-ray free electron laser. Authors: Echelmeier, A. / Cruz Villarreal, J. / Messerschmidt, M. / Kim, D. / Coe, J.D. / Thifault, D. / Botha, S. / Egatz-Gomez, A. / Gandhi, S. / Brehm, G. / Conrad, C.E. / Hansen, D.T. / Madsen, C. ...Authors: Echelmeier, A. / Cruz Villarreal, J. / Messerschmidt, M. / Kim, D. / Coe, J.D. / Thifault, D. / Botha, S. / Egatz-Gomez, A. / Gandhi, S. / Brehm, G. / Conrad, C.E. / Hansen, D.T. / Madsen, C. / Bajt, S. / Meza-Aguilar, J.D. / Oberthur, D. / Wiedorn, M.O. / Fleckenstein, H. / Mendez, D. / Knoska, J. / Martin-Garcia, J.M. / Hu, H. / Lisova, S. / Allahgholi, A. / Gevorkov, Y. / Ayyer, K. / Aplin, S. / Ginn, H.M. / Graafsma, H. / Morgan, A.J. / Greiffenberg, D. / Klujev, A. / Laurus, T. / Poehlsen, J. / Trunk, U. / Mezza, D. / Schmidt, B. / Kuhn, M. / Fromme, R. / Sztuk-Dambietz, J. / Raab, N. / Hauf, S. / Silenzi, A. / Michelat, T. / Xu, C. / Danilevski, C. / Parenti, A. / Mekinda, L. / Weinhausen, B. / Mills, G. / Vagovic, P. / Kim, Y. / Kirkwood, H. / Bean, R. / Bielecki, J. / Stern, S. / Giewekemeyer, K. / Round, A.R. / Schulz, J. / Dorner, K. / Grant, T.D. / Mariani, V. / Barty, A. / Mancuso, A.P. / Weierstall, U. / Spence, J.C.H. / Chapman, H.N. / Zatsepin, N. / Fromme, P. / Kirian, R.A. / Ros, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u57.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u57.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 6u57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/6u57 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u57 | HTTPS FTP |
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-Related structure data
Related structure data | 1x8fS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1660970 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30870.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria) Strain: B / BL21-DE3 / Gene: kdsA, ECBD_2406 / Plasmid: pET-23d / Production host: Escherichia coli (E. coli) References: UniProt: A0A140N8Q6, UniProt: P0A715*PLUS, 3-deoxy-8-phosphooctulonate synthase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.47 % Description: uniform crystals ranging between 8 and 10 micrometers |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.3 Details: 8.75-12 mg/mL KDO8PS in 20 mM Tris-HCl pH=7.3, 125 mM KCl, 2 mM beta-mercaptoethanol with 16-20% w/v poly(ethylene glycol) methyl ether |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3316 Å |
Detector | Type: AGIPD / Detector: PIXEL / Date: Sep 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3316 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48 Å / Num. obs: 6888 / % possible obs: 100 % / Redundancy: 184.2 % / Biso Wilson estimate: 84.6 Å2 / CC1/2: 0.6367 / R split: 0.143 / Net I/σ(I): 4.61 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 147.4 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 674 / CC1/2: 0.4168 / R split: 1.212 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 300 µm2 / Pulse duration: 100 fsec. / Pulse energy: 280 µJ / Pulse photon energy: 9.3 keV / XFEL pulse repetition rate: 320 Hz |
Serial crystallography sample delivery | Description: droplet in oil / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: fluorinated oil / Description: droplet in oil GDVN infection / Flow rate: 8 µL/min / Jet diameter: 7.5 µm |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X8F Resolution: 2.8→48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 24.441 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.25 Å2 / Biso mean: 89.936 Å2 / Biso min: 44.23 Å2
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Refinement step | Cycle: final / Resolution: 2.8→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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